Tuesday, October 09, 2012

A Dishonest Intelligent Design Proponent?

Most IDiots are ignorant about evolution and they let their religious biases interfere with the proper interpretation of scientific data. We excuse their mistakes on the grounds that they don't know any better.

However, some IDiots clearly should know better. They have advanced degrees in relevant fields and they have received considerable feedback on the claims they post or the books they write. We know they have read the critiques so when they persist in repeating falsehoods, there must be another explanation. They must be lying.

Jonathan Wells has a Ph.D. in molecular biology. He has posted numerous articles about junk DNA and he was written a book on the subject (The Myth of Junk DNA). Lots of people have made comments about his blog posts and his book has been widely critiqued. Many of his claims have been shown to be false.

So what do we make of his recent post on Evolution News & Views) (sic) entitled Why All the Fuss Over Some Junk?. We are forced to conclude that Wells is dishonest. Perhaps with the caveat expressed by Peter Medawar many years ago in his review of Père Teihard's The Phenomenon of Man.

Yet the greatest part of it, I shall show, is nonsense, tricked out with a variety of metaphysical conceits, and its author can be excused of dishonesty only on the grounds that he has taken great pains to deceive himself.

Some historical context might help. After James Watson and Francis Crick discovered the molecular structure of DNA in 1953, Crick announced that they had found "the secret of life," a popular formulation of which became "DNA makes RNA makes protein makes us." But biologists discovered that about 98% of our DNA does not code for protein, and in 1972 Susumu Ohno and David Comings independently used the term "junk" to refer to non-protein-coding DNA (though neither man excluded the possibility that some of it might turn out to be functional).

Many people have explained why Wells is wrong about the history of junk DNA. It has nothing to do with Wells' mangled version of the Central Dogma of Molecular Biology because we knew in the 1960s that lots of functional DNA didn't encode proteins. His history is factually incorrect.

Why didn't biologists simply call non-protein-coding sequences "DNA of unknown function" rather than "junk DNA?" For some, it was because "junk DNA" seemed more suited to the defense of Darwinism and survival of the fittest. In 1976, Richard Dawkins wrote in The Selfish Gene that "the true 'purpose' of DNA is to survive, no more and no less. The simplest way to explain the surplus [i.e., non-protein-coding] DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA."

Wells has been told that this is wrong. There was positive evidence that a lots of DNA was junk (e.g. pseudogenes, genetic load, Cot analysis, C-value paradox). Furthermore, true Darwinists, including Richard Dawkins, wanted the extra DNA to have a function. That's why the idea of selfish DNA (functional transposons) was so appealing to that group. Even today, most of us don't count active transposons as junk.

Dawkins continued to rely on junk DNA in his 2009 book The Greatest Show on Earth: The Evidence for Evolution. "It is a remarkable fact," he wrote, "that the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes." In particular, pseudogenes "are genes that once did something useful but have now been sidelined and are never transcribed or translated." Dawkins concluded: "What pseudogenes are useful for is embarrassing creationists. It stretches even their creative ingenuity to make up a convincing reason why an intelligent designer should have created a pseudogene... unless he was deliberately setting out to fool us."

But if most of our DNA is functional, as the ENCODE results suggest, then the "junk DNA" argument against ID collapses.

Wells knows full well that the presence of pseudogenes at the same loci in different species is a powerful argument for common descent and also a difficult challenge for creationists. In fact, Wells is so sensitive to this argument that he put into his book an appendix on The Vitamin C Pseudogene here he argued, among other things, that the pseudogene might be functional.

Wells must understand that the ENCODE results say nothing about the function of these sorts of pseudogenes and that the pseudogene argument is quite separate from the argument about the amount of junk in our genome. He know all this but he still posts nonsense.

27 comments
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I am not sure what department he was in, but his dissertation was in development (as I recall maybe on Xenopus early stages). From a member of his committee as told to me, it was not a very distinguished job, but it got him through and he never mentioned that he was sent there by the Rev. Moon, who apparently paid for him while he was at Berkeley.

Jonathan Wells was a PhD student in the lab of John Gerhart in the Department of Molecular and Cellular Biology at UC Berkeley in the mid 90's. He published two papers from his PhD, both as middle authors (http://www.ncbi.nlm.nih.gov/pubmed?term=Wells%20Gerhart). It could (and has) been argued that the primary goal for Jonathan at UC Berkeley was to obtain a PhD in biological science related field... and use the degree as a sword of "credibility" to fight mainstream science, rather than he taking the great opportunity offered to him by John Gerhart and others to actually expand his knowledge in biology. John Gerhart and his long term friend and colleague, Marc Kirschner (who was my PhD supervisor) have written several books in evolutionary biology, including "The Plausibility of Life: Resolving Darwin's Dilemma" and "Cells, Embryos, and Evolution: Toward a Cellular and Developmental Understanding of Phenotypic Variation and Evolutionary Adaptability". Too bad Jonathan Wells did not take the opportunity to actually learn something during his PhD.

On his behalf I offer the plea of NOT GUILTY!Why could he not be incompetent or unsmart before a no-good-nick in character??

he makes his case and expects to persuade people and be rewarded for a sharp investigation! There are conspiracy's but not is these matters.

If he's wrong just take him on!I always presume sincere convictions rule in these issues for those who place their intelligence on the line in making out a case.These are quite famous people who most likely will get more famous as time goes on.We are in a historic revolution/rebellion in origin subjects that is unlike other areas of "science".The whole world is watching this and knows there is a chance for a great fall in old ideas.Once again!

It's so unlikely that he is making a wilfull falsehood!He surely thinks he's making a good point!He expects to persuade and be seen by his fellow creationists and everyone as a insightful thinker on these things.In origin subjects or everything people not agreeing always makes everyone frustrated but its usually just human nature or error that is the culprit!I get frustrated and suspicious but things written in public by people who expect to persuade is usually coming from sincere opinion.Just defending my gang(s) buthuman error is a study in itself.

IMHO it doesn't matter if Wells' degree is in embryology or in molecuar biology. With a PhD in any field of biology he should have learned how science works, how to find, read and properly cite relevant references and what integrity and honesty mean for science. Starting from religion based premises, cherry picking and quote mining the literature Wells is not only denying the exisance of junk DNA but he indeed is undermining biological sciences in their intirety. All he has published since he finished his PhD must be a slap in the faces of his supervisors.

Have you actually read Jonathan Wells's book? Stephen Meyer's book? Michael Behe's book? You say here that Jonathan Wells has been found out lying? That is all good and fair but can you cite these sources? I mean I can also go around and call Prof Larry Moran a big fat liar without substantiating my claim and that is not exactly fair to you now is it?

Lastly have you noticed you're trying the age old divide and conquer tactic with your two recent posts?

In some cases there really is a right answer while in other cases there's a genuine scientific controversy. I'm happy to debate the questions that are really controversial but when the correct answer is known, I expect people to 'fess up and admit that they slipped up.

There is a little box/field at the top of this blogs that is labeled with a magnifying glass. If you type "jonathan wells" in it, then hit "enter," it will produce blog entries where this famous IDiot (Wells, of course) is mentioned. Browse through that and you will find some reviews, at least one is chapter-by-chapter, of at least two books written by Jonathan Wells. (Since I don't give a damn about Jonathan's pile of crap I did not browse much more.)

Andre: Many people would refuse to discuss such stuff at all lest it be dignified. I think the ID camp ought to be grateful to Prof. Moran for devoting so much time and effort to read and review those books. They would also do well to familiarise themselves with the reviews and the instructive critique therein.

Since you obviously don't accept the theory of evolution, will you describe in detail what you think is responsible for the diversity of life and what your background is that enables you to discern that the theory of evolution is wrong and that your beliefs are correct?

"Just like 440 Encode scientists are all wrong because Pro Moran said so!"

You obviously haven't been paying attention. Larry didn't say that 440 Encode scientists are wrong. He said that the ones who are claiming the Encode studies show that most or all 'junk' DNA is functional are wrong. Some of the Encode scientists have stated that the Encode studies do not support the claim that most or all 'junk' DNA is functional.

Andy: Larry really does need to respond to that comment John M made, because it seems to catch him in a glaring contradiction.

Are you suggesting that when scientists are caught in glaring contradictions, or when they are proven wrong, or when they don’t know how to answer a question, they should just pretend that the contradictions or the inconvenient questions do not exist?

To those of you who ask if Larry if has "read the book", I ask this question: How many of the thousands of books on evolution have you read? How many of the hundreds of thousands of peer-reviewed journal articles? Why do we always have to "read your book" (or in the case of Expelled, see your movie)? When you have done some real work, please let us know - and please start with research, not blogs, books or movies.

Matt G: Are you offering to fund the lab and work? With that aside, it seems to be a reasonable question to ask a critic if he or she had read, seen, etc, what is being critiqued. That question hardly requires that you to read every book, blog, or movie that is suggested, or even the work in question.

ID has added NOTHING to our knowledge or understanding of biology. No book which defends ID has ever added anything because there is nothing to add. Normally I would agree that one should read a book before critiquing it, but not in the case of ID or any other pseudoscience. Reworking BS just gives more BS. If you have something to say, say it with evidence, not sophistry. There are legitimate disagreements in biology, but ID is not one of them.

I'm reminded of the early days of ID. The Templeton Foundation got wind of ID and made money available for ID research. They received ZERO applications! ID supporters have NEVER come up with a testable hypothesis, so what would ID "research" look like?

That is a fair question and is certainly a problem that the ID community needs to address in order to have credence within the scientific community. It may be, by definition, that ID is not actually testable except by inference.

Using inferential methods means that you know or assume that your premises are valid.

And of course the premises of ID have no supporting evidence and in fact a plethora of evidence to the contrary. That's assuming you can get an IDiot to actually state what the premises are other than arguments from ignorance and personal credulity. Once in a while you'll find one that's honest enough to admit that it all boils down to god (and in that case it's always the god that that particular IDiot was indoctrinated in) did it but those are few and far between.

And while we are at it, just where are the therapies and treatments from ID based research ? Given ongoing IDiot predictions of the demise of Darwinian evolution you'd think that there would be a non stop stream of technical advances coming out of IDiot laboratories and research centers. I mean, just based on ground breaking IDiot work in the junk DNA area we should be seeing a cure for cancer and old age.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.